MolNFT v1 · #69184 · protein
The crystal structures of two fragments truncated from 5-bladed beta- propeller lectin, tachylectin-2 (LIB2-D2-15)
3KIH · 5-bladed beta-propeller lectin: “The crystal structures of two fragments truncated from 5-bladed beta- propeller lectin, tachylectin-2…”. X-ray diffraction, 1 ligand (GDL), 4 pockets (best druggability 0.78). MolNFT v1 #69184 on…
- PDB
- 3KIH
- Type
- protein
- Length
- 457 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-bladed beta-propeller lectin
- Ligands
- GDL
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | 5-bladed beta-propeller lectin | protein | 90 | 14% helix, 40% strand | — |
| B | 5-bladed beta-propeller lectin | protein | 95 | 15% helix, 36% strand | — |
| C | 5-bladed beta-propeller lectin | protein | 91 | 11% helix, 37% strand | — |
| D | 5-bladed beta-propeller lectin | protein | 91 | 12% helix, 37% strand | — |
Ligands and binding sites
- GDL · 2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.78 | 0.85 | 36 | empty |
| 2 | 631 | 0.78 | 0.83 | 43 | empty |
| 3 | 249 | 0.56 | 0.78 | 35 | empty |
| 4 | 50 | 0.37 | 0.81 | 17 | empty |
Interfaces
8 interfaces between chains.
- C–E · 1582 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 687 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 634 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 627 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 610 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3KIH · The crystal structures of two fragments truncated from 5-bladed beta-propeller lectin… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3KIH · PDBe 3KIH
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